bump to 24.1 - Single-container setup

.github/workflows/lint.yml

@@ -5,18 +5,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
-    - name: Cleanup to only use compose
-      run: rm -R docs galaxy test
+      uses: actions/checkout@v4
+    # - name: Cleanup to only use compose
+    #   run: rm -R docs galaxy test
     - name: Run shellcheck with reviewdog
-      uses: reviewdog/action-shellcheck@v1.1.3
+      uses: reviewdog/action-shellcheck@v1.27.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         reporter: github-check
         level: warning
         pattern: "*.sh"
     - name: Run hadolint with reviewdog
-      uses: reviewdog/action-hadolint@v1.16.0
+      uses: reviewdog/action-hadolint@v1.46.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         reporter: github-check

.github/workflows/single.sh

@@ -19,6 +19,7 @@ docker info
 
 # start building this repo
 git submodule update --init --recursive
+git submodule update --remote --rebase
 sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
 
 ## define a container size check function, first parameter is the container name, second the max allowed size in MB
@@ -50,8 +51,8 @@ docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \
     --privileged=true \
     -v "$(pwd)/local_folder:/export/" \
     -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
-    -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True \
-    -e GALAXY_CONFIG_ENABLE_USER_DELETION=True \
+    -e GALAXY_CONFIG_ALLOW_PATH_PASTE=True \
+    -e GALAXY_CONFIG_ALLOW_USER_DELETION=True \
     -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
     -v /tmp/:/tmp/ \
     quay.io/bgruening/galaxy
@@ -82,7 +83,7 @@ cd "${WORKING_DIR}/test/slurm/" && bash test.sh && cd "$WORKING_DIR"
 # - cd $WORKING_DIR/test/gridengine/ && bash test.sh && cd $WORKING_DIR
 
 echo 'Waiting for Galaxy to come up.'
-galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 300
+galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 600
 
 curl -v --fail $BIOBLEND_GALAXY_URL/api/version
 
@@ -124,7 +125,7 @@ cd "$WORKING_DIR/test/bioblend/" && . ./test.sh && cd "$WORKING_DIR/"
 #  then
 #    # Test without install-repository wrapper
 #      sleep 10
-#      docker_exec_run bash -c 'cd $GALAXY_ROOT && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
+#      docker_exec_run bash -c 'cd $GALAXY_ROOT_DIR && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
 #  fi
 
 

.github/workflows/single_container.yml

@@ -1,15 +1,15 @@
 name: Single Container Test
-on: [push]
+on: [push, pull_request]
 jobs:
   build_and_test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ['3.10']
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
-    - uses: actions/setup-python@v1
+      uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Build and Test

.gitmodules

@@ -1,7 +1,8 @@
 [submodule "galaxy/roles/galaxyproject.galaxyextras"]
 	path = galaxy/roles/galaxyprojectdotorg.galaxyextras
-	url = https://github.com/galaxyproject/ansible-galaxy-extras
-        branch = 20.05
+	url = https://github.com/jyotipm29/ansible-galaxy-extras
+	branch = 24.1
+
 [submodule "galaxy/roles/galaxy-postgresql"]
 	path = galaxy/roles/galaxy-postgresql
 	url = https://github.com/galaxyproject/ansible-postgresql

.travis.yml

@@ -1,14 +1,14 @@
 sudo: required
 
 language: python
-python: 3.6
+python: 3.10
 
 services:
   - docker
 
 env:
   matrix:
-    - TOX_ENV=py36
+    - TOX_ENV=py310
   global:
     - secure: "SEjcKJQ0NGXdpFxFhLVlyJmiBvgiLtR5Uufg90Vm3owKlMy0NSfIrOR+2dwNniqOp7QI3eVepnqjid/Ka0QStzVqMCe55OLkJ/TbTHnMLpbtY63mpGfogVRvxMMAVpzLpcQqtJFORZmO/MIWSLlBiXMMzOg3+tbXvQXmL17Rbmw="
 
@@ -39,6 +39,7 @@ before_install:
 
   # start building this repo
   - git submodule update --init --recursive
+  - git submodule update --remote --rebase
   - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
   - export WORKING_DIR="$TRAVIS_BUILD_DIR"
   - export DOCKER_RUN_CONTAINER="quay.io/bgruening/galaxy"
@@ -68,8 +69,8 @@ before_install:
         --privileged=true \
         -v `pwd`/local_folder:/export/ \
         -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
-        -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True \
-        -e GALAXY_CONFIG_ENABLE_USER_DELETION=True \
+        -e GALAXY_CONFIG_ALLOW_PATH_PASTE=True \
+        -e GALAXY_CONFIG_ALLOW_USER_DELETION=True \
         -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
         -v /tmp/:/tmp/ \
         quay.io/bgruening/galaxy
@@ -101,7 +102,7 @@ script:
   # - cd $TRAVIS_BUILD_DIR/test/gridengine/ && bash test.sh && cd $WORKING_DIR
 
   - echo 'Waiting for Galaxy to come up.'
-  - galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 300
+  - galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 600
 
   - curl -v --fail $BIOBLEND_GALAXY_URL/api/version
 
@@ -140,7 +141,7 @@ script:
   #  then
   #      # Test without install-repository wrapper
   #      sleep 10
-  #      docker_exec_run bash -c 'cd $GALAXY_ROOT && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
+  #      docker_exec_run bash -c 'cd $GALAXY_ROOT_DIR && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
   #  fi